ggtree

DOI: 10.18129/B9.bioc.ggtree  

an R package for visualization of tree and annotation data

Bioconductor version: Release (3.16)

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

Author: Guangchuang Yu [aut, cre, cph] , Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] , Lin Li [ctb], Bradley Jones [ctb], Justin Silverman [ctb], Watal M. Iwasaki [ctb], Yonghe Xia [ctb], Ruizhu Huang [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggtree")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ggtree")

 

HTML	R Script	ggtree
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization
Version	3.6.2
In Bioconductor since	BioC 3.1 (R-3.2) (8 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.0.6), yulab.utils, tidyr, tidytree (>= 0.3.9), treeio(>= 1.8.0), utils, scales, stats, cli
LinkingTo
Suggests	emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue
SystemRequirements
Enhances
URL	https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/(book) http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628(paper)
BugReports	https://github.com/YuLab-SMU/ggtree/issues
Depends On Me	ggtreeDendro, tanggle
Imports Me	cardelino, cogeqc, enrichplot, ggmsa, ggtreeExtra, LinTInd, LymphoSeq, miaViz, microbiomeMarker, MicrobiotaProcess, orthogene, philr, scBubbletree, singleCellTK, sitePath, systemPipeTools, treekoR
Suggests Me	compcodeR, syntenet, TreeAndLeaf, treeio, TreeSummarizedExperiment, universalmotif
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ggtree_3.6.2.tar.gz
Windows Binary	ggtree_3.6.2.zip
macOS Binary (x86_64)	ggtree_3.6.2.tgz
macOS Binary (arm64)	ggtree_3.6.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ggtree
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ggtree
Bioc Package Browser	https://code.bioconductor.org/browse/ggtree/
Package Short Url	https://bioconductor.org/packages/ggtree/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.16	Source Archive